Insights into data transformation

[Thapeachydude]

Hi,

I was wondering if you have anymore insights/guidance on the data transformation.
I have a spectral flow cytometry data set, that a collaborator acquired. I've tried the general 150 co-factor, most markers look Ok this way, but individual ones now have a very weird "negative" smear.

Have you had this issue before and is there any good way to judge the quality of the transformation? (besides just looking at it)?

Happy for any insights!

Cheers

[SamGG]

Hi,
diffcyt is not really dealing with data transformation. I don't know which spectral instrument acquired those data, but I think the co-factor is too low. To tune it correctly, follow the discussion and guidance in Liechti et al. , especially fig2 d & e.
Best.

[Thapeachydude]

Hi,
thanks for the quick reply! That indeed proved to be quite helpful!